I am currently trying to test the effectiveness of various thermal compounds (TIMs) on cpu processors. I am currently trying to find the thinnest thermal probe/thermocouple I can find for this project.
My current idea is that I could place one prob ontop of the CPU and then apply the thermal compound. I would then place another probe and then attach the heatsink.

From there I could measure the heatchange and calculate the thermal conductivity of the product.

I have seen many techniques that would first take the processor and mill out a canal in the casing of the processor to place the thermocouple inside, but I am hoping that there is another way

I don't know if I would attempt to place a prob there as it will defeat the purpose and cause a air gap , and to be honest I see no real difference in temps between any fancy TIM or plain old thermal paste that I have used and apparently mayonnaise is a good alternative LOL

Your best option is a laser thermometer if you want precise measurements, putting a probe on the CPU directly will result in a bad mount. Trust me, I did that once with a GPU and a fan controller and i cooked the GPU and the motherboard.

Why are you trying to find that info out ? I did link you in my above post to a pretty thorough comparison of different TIMs from high end stuff to Mayonnaise and there was only a 3 deg difference from the top performer to Mayonnaise , now we know lipstick is not a very good TIM but it was still with in a few deg of all the name brand stuff ....

But if you determined to find it out Superflyx3 gave you a pretty decent suggestion about using a laser thermometer..

lol sorry i didn't click on the mayonaise bit since i thought it was a joke.

I guess i could use an IR thermometer but I am ultimately unsure of what points to measuring with that approach since I would be unable to read the temp of the center of the die, or the temp of where the heat sink comes in contact with the TIM.